A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae

Molecular Systems Biology

Volumn 3, Issue , 2007, Pages

  Grilly, Chris ^a   Stricker, Jesse ^a   Pang, Wyming Lee ^a,c   Bennett, Matthew R ^a,b   Hasty, Jeff ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Gene regulation; Temporal dynamics

Indexed keywords

BACTERIAL PROTEIN; SYNTHETIC DNA; ADENOSINE TRIPHOSPHATASE; CHAPERONE; CLPX PROTEIN, E COLI; ENDOPEPTIDASE CLP; ESCHERICHIA COLI PROTEIN; GREEN FLUORESCENT PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; ENZYME MECHANISM; ESCHERICHIA COLI; FLUORESCENCE; GENE ACTIVATION; GENE CONTROL; GENE REPRESSION; GENETIC REGULATION; HALF LIFE TIME; MICHAELIS MENTEN KINETICS; MICROBIAL ACTIVITY; MICROFLUIDIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN STRUCTURE; REPORTER GENE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; CYTOLOGY; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PROTEIN PROCESSING;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

ADENOSINE TRIPHOSPHATASES; ENDOPEPTIDASE CLP; ESCHERICHIA COLI PROTEINS; GENE REGULATORY NETWORKS; GREEN FLUORESCENT PROTEINS; MOLECULAR CHAPERONES; PROTEIN PROCESSING, POST-TRANSLATIONAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 34547607675     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100168     Document Type: Article

References (23)

1. Andersen JB, Sternberg C, Poulsen LK, Bjørn SP, Givskov M, Molin S (1998) New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol 64: 2240-2246
2. Bennett MR, Pang WL, Ostroff NA, Tsimring LS, Hasty J (2007) Metabolic gene regulation in a dynamically changing environment (submitted)
3. Blake WJ (2003) Development of artificial gene regulatory networks in Saccharomyces cerevisiae: genetic switches and noise modulation. PhD Thesis, Boston University
4. Cookson S, Ostroff N, Pang WL, Volfson D, Hasty J (2005) Monitoring dynamics of single-cell gene expression over multiple cell cycles. Mol Syst Biol 1: 2005.0024
5. Cronin CA, Gluba W, Scrable H (2001) The lac operator-repressor system is functional in the mouse. Genes Dev 15: 1506-1517
6. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8
7. Gottesman S, Roche E, Zhou Y, Sauer RT (1998) The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev 12: 1338-1347
8. Hackett EA, Esch RK, Maleri S, Errede B (2006) A family of destabilized cyan fluorescent proteins as transcriptional reporters in S. cerevisiae. Yeast 23: 333-349
9. Hasty J, McMillen D, Collins JJ (2002) Engineered gene circuits. Nature 420: 224-230
10. Hersch GL, Baker TA, Sauer RT (2004) SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc Natl Acad Sci USA 101: 12136-12141
11. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691
12. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934
13. Kang SG, Ortega J, Singh SK, Wang N, Huang NN, Steven AC, Maurizi MR (2002) Functional proteolytic complexes of the human mitochondrial ATP-dependent protease, hClpXP. J Biol Chem 277: 21095-21102
14. Karzai AW, Roche ED, Sauer RT (2000) The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol 7: 449-455
15. Mateus C, Avery SV (2000) Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast 16: 1313-1323
16. McGinness KE, Baker TA, Sauer RT (2006) Engineering controllable protein degradation. Mol Cell 9: 701-707
17. Sambrook J, Russell DW (2001) Molecular Cloning: a Laboratory Manual. CSHL Press: Cold Spring Harbor, NY, USA
18. Sawano A, Miyawaki A (2000) Directed evolution of green fluorescent protein by a new versatile PCR strategy for site-directed and semirandom mutagenesis. Nucleic Acids Res 28: e78
19. Sheff MA, Thorn KS (2004) Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21: 661-670
20. Sprinzak D, Elowitz MB (2005) Reconstruction of genetic circuits. Nature 438: 443-448
21. van Dyck L, Dembowski M, Neupert W, Langer T (1998) Mcx1p, a ClpX homologue in mitochondria of Saccharomyces cerevisiae. FEBS Lett 438: 250-254
22. Volfson D, Marciniak J, Blake WJ, Ostroff N, Tsimring LS, Hasty J (2006) Origins of extrinsic variability in eukaryotic gene expression. Nature 439: 861-864
23. Xia YN, Whitesides GM (1998) Soft lithography. Angew Chem Int Edit 37: 550-575